[gmx-users] Reducing density using -vdwd option for a new solvent in the system

[Justin A. Lemkul]

shivangi nangia wrote:
> Dear Justin,
> 
> I have run into another problem.
> 
> I created the system by including DHB in vwdradii.dat as follows:
> 
> ; Very approximate VanderWaals radii
> ; only used for drawing atoms as balls or for calculating atomic overlap.
> ; longest matches are used
> ; '???' or '*' matches any residue name
> ; 'AAA' matches any protein residue name
> ???  C     0.15
> ???  F     0.12
> ???  H     0.04
> ???  N     0.110
> ???  O     0.105
> ???  S     0.16
> *DHB  C     0.5
> DHB  H     0.5
> DHB  O     0.5*
> ; Water charge sites
> SOL  MW    0
> SOL  LP    0
> ; Masses for vsite construction
> GLY  MN1   0
> GLY  MN2   0
> ALA  MCB1  0
> ALA  MCB2  0
> VAL  MCG1  0
> VAL  MCG2  0
> ILE  MCG1  0
> ILE  MCG2  0
> ILE  MCD1  0
> ILE  MCD2  0
> LEU  MCD1  0
> LEU  MCD2  0
> MET  MCE1  0
> MET  MCE2  0
> TRP  MTRP1 0
> TRP  MTRP2 0
> THR  MCG1  0
> THR  MCG2  0
> LYSH MNZ1  0
> LYSH MNZ2  0
> 
> After making this change, DHB molecules were not over lapping with each 
> other.
> 
> I tried to energy minimized the system.
> minim.mdp
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator  = steep     ; Algorithm (steep = steepest descent minimization)
> ;emtol    = 1000.0    ; Stop minimization when the maximum force < 
> 1000.0 kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps      = 50000     ; Maximum number of (minimization) steps to perform
> 
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist     = 1      ; Frequency to update the neighbor list and long 
> range forces
> ns_type     = grid      ; Method to determine neighbor list (simple, grid)
> rlist    = 1.0    ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME    ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0    ; Short-range electrostatic cut-off
> rvdw     = 1.0    ; Short-range Van der Waals cut-off
> pbc      = xyz       ; Periodic Boundary Conditions (yes/no)
> constraints = none
> 
> 
>  After about 6000 steps the run stops with the message:
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> 
> Double precision normally gives you higher accuracy.
> 
> Steepest Descents converged to machine precision in 6012 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  1.0655116e+05
> Maximum force     =  1.6512177e+02 on atom 2076
> Norm of force     =  6.5337501e+00
> 
> 
> 
> The potential energy is high, but I still continued to equilibration.
> After NVT equilibration, NVT equilbration runs into the following error 
> as soon it starts:
> 
> 
> Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which 
> is larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> /var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC 
> <http://1869547.lionxj.rcc.psu.edu.SC>: line 14:  2359 Segmentation 
> fault      mdrun -deffnm npt
> 
> 
> 
> 
> So, I have three questions:
> 
> 1. Is the starting structure bad?

Probably.

> 2. Did I change the vdwd radii by a lot (0.105 to 0.5)

Yes.  And you shouldn't use those artificial values for anything else.  Remove 
them after you've inserted the DHB into your system.  This is, of course, no 
guarantee that the system is stable, either.

> 3. What value of table extension should be used for 1-4 interaction ( 
> default value is?) if thats the problem to be fixed.
> 

Do not adjust the table extension.  If the system is blowing up, there's no 
reason to troubleshoot the constraints; they're not your problem.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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